Kenya SHS Round 1

1 Objective

The objective of this analysis is to identify potential data quality issues with in coming Kenya soil health round 1 study data so that the enumeration team can address issues in the field and improve overall quality. This file will also serve as (1) an initial cleaning file and (2) an attrition and balance check to inform when to wrap up enumeration.

2 Key Takeaways

1. We have likely outliers in the numeric data. Follow up with enumerators about these values.
2. Many round 1 GPS points are not close to the baseline value. Follow up about plot continuity and GPS quality. (see Kenya round 1 data check)

rm(list = ls())
cat("\014")



## set up some global options
# always set stringsAsFactors = F when loading data
options(stringsAsFactors=FALSE)
# show the code
knitr::opts_chunk$set(echo = TRUE)
# define all knitr tables to be html format
options(knitr.table.format = 'html')
# change code chunk default to not show warnings or messages
knitr::opts_chunk$set(warning = FALSE, message = FALSE)
libs <- c("dplyr", "reshape2", "knitr", "ggplot2", "tibble", "readxl", 
    "MASS", "gridExtra", "cowplot", "robustbase", "car", "RStata", "foreign",
    "tidyr", "readxl", "stringr", "sp", "dismo", "leaflet", "XML", "ggmap", "knitr",
    "MASS")
lapply(libs, require, character.only = T, quietly = T, warn.conflicts = F)

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#### define helpful functions
# define function to adjust table widths
html_table_width <- function(kable_output, width) {
  width_html <- paste0(paste0('<col width="', width, '">'), collapse = "\n")
  sub("<table>", paste0("<table>\n", width_html), kable_output)
}
source("../oaflib/commcareExport.R")
source("../oaflib/misc.R")

3 Data

3.1 Import round 1 data

I’m going to use the CommCare API created by Robert On to access the data directly from CommCare. This ensures that there are no changes to the data between the point of access and the point of cleaning and analysis

forceUpdateAll = F
forceUpdate = forceUpdateAll
d <- getFormData("harvest", "Soil Sampling", "Soil Sampling 2017", forceUpdate)

[1] "found 677cf904ae87a358b18d0ad453b747d"

Duplicated column names deduplicated: 'District Name' => 'District Name_1' [20], 'Site Name' => 'Site Name_1' [21], 'Last Name' => 'Last Name_1' [22], 'First Name' => 'First Name_1' [23], 'Client Phone' => 'Client Phone_1' [24], 'What seed type did you use on this plot?' => 'What seed type did you use on this plot?_1' [53], 'How many kgs of seed did you use?' => 'How many kgs of seed did you use?_1' [54], 'Measurement of the reported yield/quantity' => 'Measurement of the reported yield/quantity_1' [56], 'What fertilizer did you use on your ____ for the long rains 2016?' => 'What fertilizer did you use on your ____ for the long rains 2016?_1' [63], 'How many KGs of CAN did you apply to the ____?' => 'How many KGs of CAN did you apply to the ____?_1' [65], 'How many KGs of NPK did you apply to the ____?' => 'How many KGs of NPK did you apply to the ____?_1' [66], 'How many KGs of urea did you apply to the ____?' => 'How many KGs of urea did you apply to the ____?_1' [67]Parsed with column specification:
cols(
  .default = col_character(),
  metadata.deviceID = col_double(),
  metadata.timeStart = col_datetime(format = ""),
  metadata.timeEnd = col_datetime(format = ""),
  `Are you or household member a member of OAF 2017?` = col_integer(),
  `OAF ID` = col_integer(),
  `Respondent's approximate age` = col_integer(),
  `Respondent's Gender` = col_integer(),
  `Number of people in this Household(Include respondent).` = col_integer(),
  `How many seasons have you participated with One Acre Fund, including this long rains 2017 season?` = col_integer(),
  `How many cows do you own?` = col_integer(),
  `How many goats do you own?` = col_integer(),
  `How many chickens do you own?` = col_integer(),
  `How many pigs do you own?` = col_integer(),
  `How many sheep do you own?` = col_integer(),
  `Please choose the closest field size` = col_double(),
  `How many kgs of seed did you use?` = col_double(),
  `What was the yield for this plot?` = col_double(),
  `How would you describe your long rains 2016 harvest in this field compared to previous long rains seasons?` = col_integer(),
  `How many kgs of seed did you use?_1` = col_double(),
  `What was the yield for this intercrop?` = col_double()
  # ... with 12 more columns
)
See spec(...) for full column specifications.

# add in force update to get latest report

3.2 Import baseline

baselineDir <- normalizePath(file.path("..", "ke_baseline", "data"))
b <- read.csv(file=paste0(baselineDir, "/shs ke baseline.csv")) # obj d

3.3 Import soil data

Here I access the soil predictions from the OAF soil lab. Patrick Bell manages the lab and Mike Barber oversees the prediction scripts.

soilDir <- normalizePath(file.path("..", "..", "OAF Soil Lab Folder", "Projects", "ke_shs_17", "4_predicted", "other_summaries"))
soil <- read.csv(file=paste(soilDir, "combined-predictions-including-bad-ones.csv", sep = "/"))
idDir <- normalizePath(file.path("..", "..", "OAF Soil Lab Folder", "Projects", "ke_shs_17", "5_merged"))
Identifiers <- read_excel(paste(idDir,"Soil Sampling - Sample reception 2017 - Sample reception 20172017-04-12 (1).xlsx",sep="/"), sheet=1) %>%
  mutate(
    reception_barcode = gsub("_", "", reception_barcode)
  )
soil$SSN[!soil$SSN %in% Identifiers$reception_barcode]

[1] "oafke002126"

Identifiers$reception_barcode[!Identifiers$reception_barcode %in% soil$SSN]

[1] "oafke0001485" "oafke0002126"

It seems to be the case that one barcode is not matching due to the number of zeros. Correct and update.

soil$SSN[soil$SSN=="oafke002126"] <- "oafke0002126"

There’s one record in the Identifiers that doesn’t appear in the data. An extra sample without a survey? Seems odd.

3.4 Update variable names

The variable names are out of control. In order to make the variable names more user friendly, I went to CommCare and downloaded the form contents that includes the variable name. I then wrote in a more user friendly variable name in the file. I import and overwrite the variable names here. Perhaps there’s a better way to do this but it’s easier to log the changes in excel than to write out all the code. The reference files will be on hand in case I accidentally mislabel a variable. The variable names in the excel file start with variable 11 from CommCare. The first 10 CommCare variables are meta data which we will keep.

General TODO

• import round 1 soil data
• do some cleaning and checking of round 1 data
• import baseline data
• align baseline and round 1 data long

newName <- read_excel("var_names.xlsx", sheet=1)

qTypes <- c("Multiple Choice", "Phone Number or Numeric ID", "Checkbox", "Text", "Decimal", "Image Capture", "Barcode Scan", "GPS", "Integer")
newName <- newName %>% dplyr::select(1:4
) %>% dplyr::filter(newName$Type %in% qTypes) %>% as.data.frame()
newName <- newName %>% filter(new.var.name!="general.comment")

Keep the participation variable in d so we understand who agreed to participate. Make additional changes to d to prepare it to be combined with the meta information from CommCare.

names(d)[26] <- "participation"
names(d)[names(d)=="#form/id_base/Soil_Sample_Id"] <- "Soil_Sample_Id"
names(d)[names(d)=="#form/id_2017new/Soil_Sample_Id"] <- "New_soil_sample_id"

Merge in variable names to check that they match and then replace names(). I’m subtracting two because the Soil_Sample_Id variables appear out of order.

I’m also adding some variables to the new name vector as d now has a different variable length

newNameVec <- c(newName$new.var.name[1], "agree", "interviewed.2016", "refusal", newName$new.var.name[2:(length(newName$new.var.name)-1)], "comment", newName$new.var.name[length(newName$new.var.name)])
names(d)[11:(length(d)-3)] <- newNameVec
# drop vars with drop
d <- d[,-which(grepl("drop.", names(d)))]

Make new variables

#convert acreage to m2 and then calculate fertilizer per acre
d$plot.m2 <- d$plot.size*4046
m2ToAcres <- function(input, meters) {
  res <- (input/meters)*4046
  return(res)
}
d$can.acre <- m2ToAcres(d$can.main, d$plot.m2)
d$dap.acre <- m2ToAcres(d$dap.main,d$plot.m2)
d$npk.acre <- m2ToAcres(d$npk.main,d$plot.m2)
d$urea.acre <- m2ToAcres(d$urea.main,d$plot.m2)
d$compost.acre <- m2ToAcres(d$compost.kgs,d$plot.m2)
d$seed.acre <- m2ToAcres(d$seed.kgs,d$plot.m2)
d$intercrop.seed.acre <- m2ToAcres(d$intercrop.seed.kgs, d$plot.m2)
d$intercrop.dap.acre <- m2ToAcres(d$dap.intercrop, d$plot.m2)
d$intercrop.can.acre <- m2ToAcres(d$can.intercrop, d$plot.m2)
d$intercrop.npk.acre <- m2ToAcres(d$npk.intercrop, d$plot.m2)
d$intercrop.urea.acre <- m2ToAcres(d$urea.intercrop, d$plot.m2)

Yield calculation - first let’s confirm that when the yield.unit is NA that there isn’t a yield value.

table(d$yield[is.na(d$yield.unit)], useNA = 'ifany')

   0 <NA> 
  24   56 

TODO - Charles: I assume a 0 yield is a true value. Or should it be NA? The code below converts all yield values associated with an NA unit to NA when in fact there should be some 0s.

d$yield.kg <- ifelse(d$yield.unit=="100kg", d$yield*100, 
              ifelse(d$yield.unit=="50kg", d$yield*50,
              ifelse(d$yield.unit=="90kg", d$yield*90,
              ifelse(d$yield.unit=="GG", d$yield*2, NA))))

3.4.1 Import feedback

Here I take the follow up responses from enumerators and update the values in the the full data. I only want the outlier checks to show values that we haven’t already addressed through soliciting additional feedback from enumerators and farmers. This code assumes the data comes in with rows as farmers and columns as the questions that needed to be addressed. I’ve reshaped it to include

TODO - come back and figure out how to quickly add in the phone data

#updateDir <- paste(getwd(), "enum_summaries", sep = "/")
# updates <- read.csv("Phone calls survey.csv", header=T, stringsAsFactors = F) %>% rename(
#   Soil_Sample_Id = soil_sample_id,
#   age = Age.of.respondent,
#   can.intercrop = How.many.KGs.of.CAN.did.you.apply.to.the..intercrop.,
#   can.main = How.many.KGs.of.CAN.did.you.apply.to.the.main.crop.,
#   chickens = Number.of.chickens.How.many.chickens.do.you.own..chickens,
#   dap.intercrop = How.many.KGs.of.DAP.did.you.apply.to.the.intercrop.,
#   dap.main = How.many.KGs.of.DAP.did.you.apply.to.the.main.crop.,
#   hhsize = Number.of.people.in.this.Household.Include.respondent..,
#   intercrop.seed.kgs = How.many.kgs.of.seed.did.you.use.in.your.intercrop.,
#   lime.kgs = How.many.KGs.of.lime.did.you.use.on.this.plot.,
#   npk.main = How.many.KGs.of.NPK.did.you.apply.to.the.maincrop.,
#   plot.size = What.is.your.aproximate.plotsize,
#   seed.kgs = How.many.kgs.of.seed.did.you.use.in.the.Maincrop.,
#   sheep = How.many.sheep.do.you.own.,
#   urea.main = How.many.KGs.of.urea.did.you.apply.to.the.maincrop.,
#   yield = What.was.the.yield.for.this.plot.main.crop.
# ) %>% mutate(
#   yield = ifelse(yield=="N/A", NA,  ifelse(grepl("Not", yield), NA, yield)),
#   yield = ifelse(yield=="32 bags of 90 kgs", "32 bags", yield)
# )
# 
# updates$yield.unit <- sapply(updates$yield, function(x){ # separate out the unit
#   strsplit(x, " ")[[1]][2]})
# 
# updates$yield.kg <- sapply(updates$yield, function(x){ # keep only the number
#   strsplit(x, " ")[[1]][1]})
# 
# updates$yield.kg <- ifelse(grepl("bag",  updates$yield.unit), as.numeric(updates$yield)*90, ifelse(grepl("goro", updates$yield.unit),  as.numeric(updates$yield)*2.45, updates$yield))
# 
# 
# updates <- melt(updates, id.vars = c("Soil_Sample_Id", "Comments"), measure.vars = names(updates)[6:19])
# updates <- updates %>% filter(!is.na(value) | value!= " ")
# check that this works:
#print(updates[1,])

3.5 Merge soil into data

TODO - check into how many merges we’re not getting. Finalize merge report.

d$sampling.barcode <- gsub("_", "", d$sampling.barcode)
names(soil)[names(soil)=="SSN"] <- "sampling.barcode"
d <- left_join(d, soil, by="sampling.barcode")
soilVars <- names(soil)[2:21]

3.6 Outlier check

Check all numeric variables for outliers. First, it’s probably safe to replace all -99s with NA

TODO - set up outlier checks

catVars <- names(d)[sapply(d, function(x){
  is.character(x)
})]
enumClean <- function(dat, x, toRemove){
  dat[,x] <- ifelse(dat[,x] %in% toRemove, NA, dat[,x])
  return(dat[,x])
}
strTable <- function(dat, x){
  varName = x
  tab = as.data.frame(table(dat[,x], useNA = 'ifany'))
  tab = tab[order(tab$Freq, decreasing = T),]
  end = ifelse(length(tab$Var1)<10, length(tab$Var1), 10)
  repOrder = paste(tab$Var1[1:end], collapse=", ")
  out = data.frame(variable = varName,
                   responses = repOrder)
  
  return(out)
}
# clean up known values
catEnumVals <- c("-99", "-88", "- 99", "-99.0", "88", "_88", "- 88", "0.88",
                 "--88", "__88", "-88.0", "99.0")
d[,catVars] <- sapply(catVars, function(y){
  d[,y] <- enumClean(d,y, catEnumVals)
})
responseTable <- do.call(rbind, lapply(catVars, function(x){
  strTable(d, x)
}))

3.6.1 Categorical response table

A simple table to preview the values in the data. The values are ranked by frequency.

kable(responseTable, format="markdown")

variable	responses
AppFormId	/Users/mlowes/drive/data/commcare_cache/677cf904ae87a358b18d0ad453b747d
id	000ce8ff-56af-4af1-8ab3-dcaaa54fe230, 0011522b-761a-45a4-9783-c217f1e7d4d6, 00135a79-0c27-4b51-89c5-fbd6d5494e06, 0033f926-d5aa-40d5-9279-0bba42d3189b, 00723ce4-7aae-4b17-924c-54885d57a8a0, 008b1760-6518-489a-902b-c6b5d8673cf0, 00905142-2f7a-4231-a32b-0c6f9fb51261, 00b06cd5-846b-4e1b-9ff8-3fd4d7f5a37d, 00b8ff5b-32f8-4909-85e6-a81aaf2c399e, 00bc4021-2420-41c5-838f-2b97646bd24b
domain	harvest
date_header	NA
metadata.userID	280c99abbb2534baa8bd95c41c7fb47d, 036a641a60414b75155e0e4fefdf01bb, 74acd8230c1733e972169cfc7113229b, d1cb024846d35c496780e0a681cb9f92, d1cb024846d35c496780e0a681cc03c9, 942a528e8cc2dc1f7f060d152839394a, d1cb024846d35c496780e0a681cca808, bc1170b650390a876f8abb9571669788, 2ed6f14f0f5a764c0d911419565ee8ff, 28ccf07370af4faa5f15ecd64bd21c1c
metadata.username	eric.k, rachel.g, john.s, stephen.n, lazarus.m, clinton.n, dennis.k, gibson.r, florence.o, wallace.n
form.case.@case_id	43abb59751f94d51acf171d595651fa0, 548a04af36fc4790a272abcfb0c1c7e9, 54ecedd1d1074986a23d2c777d127fd3, 6fb5ac28647742e598e104db43d5b300, 8bd82fadf72542b282443cdb2e1f735b, ef006c5dc2e64d93a7b27c3aefe50009, 000e81e8014a4b8bb569f7616b3f823e, 00329d4fe2304e278c438a73757cbc7c, 0042a665dafd481d9d4f6aac8cd19b2d, 005b4ac31e5e422387906b0910c15eba
same.hh	Yes, No, NA
agree	NA, yes, no
interviewed.2016	NA, No, Yes
refusal	NA, refused
region	Western Province, Nyanza, NA, Nyanza1, Western Provinc, Western Province's, Western ProvinceE, Western Provincer
district	Gem, Butere, Rachuonyo, Kakamega (South), Lugari, Migori, Kakamega B (North), Rongo, Kisii, Busia
site	NA, Kamroth Lower, Kokwanyo West, Sigomere, lureko, Achuth, Kajulu, emangale, Kanyasrega, Kisatiru
phone	NA, 0, 0717356420, 0701313242, 0703490814, 0705337016, 0719642096, 0726211155, 0792051319, 712115910
district1	NA, Rongo, Rachuonyo, Kakamega B (North), Lugari, Suneka, Chwele, Gem, Matete, Busia
site1	NA, Kamuga, Nyang'inja, riana, Bunjosi, Burinda, Chekalini, Gongo, IKURUMA, Isongo
participation	consents, NA
which.seasons	NA, lr2016, lr2016 lr2015, lr2016 lr2015 lr2014, lr2016 lr2015 lr2014 lr2013, lr2016 lr2015 lr2014 lr2013 lr2012, lr2016 lr2015 lr2014 lr2013 lr2012 lr2011, lr2016 lr2015 lr2014 lr2013 lr2012 lr2011 lr2010, lr2015, lr2016 lr2014
plot.location	The plot is behind the farmers house, The plot is opposite the homestead of the farmer, Besides the farmer's house, behind farmers house, The plot is behind the farmer's homestead, The plot is besides the farmers house, The plot is immediately behind the farmer's house., The plot is infront of the farmers house, The plot is just behind the farmers house, behind farmers house.
own	Yes, No, NA
relation.land	NA, renting, borrowing, leasing
own.2016	Yes, No, NA
most.farming	Female, both, Male, NA
main.crop	maize, NA, fallow, other, sorghum, sugar, beans, sukuma, groundnuts
main.crop.specify	NA, Nappier grass, tobacco, cassava, cassavas, Napier grass, nappier grass, Pineapple, Tobacco
seed.type	hybrid, local, NA
yield.unit	90kg, GG, 100kg, 50kg, NA
intercrop	beans, 0, NA, groundnuts, soya, maize, sorghum, sugar, other, sweetpotatoes
intercrop.specify	NA, cassava
intercrop.seed.type	local, NA, hybrid
intercrop.yield.unit	GG, NA, 90kg, 100kg, 50kg
fertilizer.main	dap can, dap, none, NA, dap urea, dap can urea, can, can npk, can urea, other
fertilizer.intercrop	none, NA, dap, dap can, can, other, dap none, urea, npk, dap other
compost.quality	NA, good, average, poor
compost.type	NA, cow, plant_residue, goat, chicken, kitchen_waste, pig
lime	no, NA, yes_oaf, yes_outside
fertility.comp	average, morefertile, lessfertile, NA
field.location	hillside, valley, hilltop, NA
soil.type	loam, sandy, clay, NA
soil.color	brown, black, red, NA
erosion	0, napier, grad_terrace, drainage, radical_terrace, NA
fallow.yn	No, Yes, NA, dont_know
fallow.cover	NA, weeds, grasses, legumes, mixed_grasses&legumes, Bare_fallow, mixed_grasses&legumes, mixed_grasses&legumes
residues	planted_into_residues, fed_to_livestock, no_incorporation, incorporated_by_hand, sold_residue, NA
photo	NA, 1325379545882.jpg, 1325379607350.jpg, 1325380848958.jpg, 1486093019962.jpg, 1486096823433.jpg, 1486097641286.jpg, 1486176674776.jpg, 1486177274444.jpg, 1486182820463.jpg
sampling.barcode	oafke0000321, oafke0000325, oafke0000661, oafke0000940, oafke0000966, oafke0001085, oafke0002000, oafke0002265, oafke0000001, oafke0000002
comment	NA, No comment, N/A, no comment, none, No comments, non, no comments, 0, no
gps	-0.5056573852841059 34.73783778147609 1390.63 15.0, -0.6098935 34.6105897 0.0 3669.0, -0.5056573852841059 34.73783778147609 1390.63 10.0, -0.5497645 34.6277074 0.0 4821.0, -0.5843478 34.6279001 0.0 4799.0, -0.7390152 34.5656951 0.0 4553.0, -0.5504687967967642 34.73721033097699 1509.32 15.0, -0.5906037 34.7379935 0.0 3000.0, -0.598296 34.7092347 0.0 4807.0, -0.6102046 34.5573404 0.0 3965.0
#form/Sampling2017_Complete	Complete, NA
Soil_Sample_Id	NA, Butere61451, c1019, Kisii43379, Busia11633, Busia11638, Busia11913, Busia12588, Busia12982, Busia13182
New_soil_sample_id	NA, Busia25200, Butere15379, c1021, c1106, c1126, c1138, c1140, c1149, c1176

3.6.2 Categorical response graphs

repGraphs <- function(dat, x){
  tab = as.data.frame(table(dat[,x], useNA = 'ifany'))
  tab = tab[order(tab$Freq, decreasing = T),]
  print(
    ggplot(data=tab, aes(x=Var1, y=Freq)) + geom_bar(stat="identity") +
      theme(legend.position = "bottom", axis.text.x = element_text(angle = 45, hjust = 1)) +
      labs(title =paste0("Composition of variable: ", x))
  )
}
adminVars <- c(names(d)[grep("meta", names(d))],"enum_name", "photo",  "participation", "refusal", "phone",  "comment", "gps", "Soil_Sample_Id", "sampling.barcode", "id", "domain", "date_header", "form.case.@case_id", "site", "district1", "site1", "plot.location", "New_soil_sample_id", "#form/Sampling2017_Complete", "AppFormId")
nonAdminVars <- catVars[!catVars %in% adminVars]
for(i in 1:length(nonAdminVars)){
  repGraphs(d, nonAdminVars[i])
}

3.7 Numeric variables

numVars <- names(d)[sapply(d, function(x){
  is.numeric(x)
})]

Basic cleaning of known issues like enumerator codes for DK, NWR, etc.

enumVals <- c(-88,-85, -99)
d[,numVars] <- sapply(numVars, function(y){
  d[,y] <- enumClean(d,y, enumVals)
})

3.7.1 Numeric outlier table

iqr.check <- function(dat, x) { 
  q1 = summary(dat[,x])[[2]]
  q3 = summary(dat[,x])[[5]] 
  iqr = q3-q1
  mark  = ifelse(dat[,x] < (q1 - (1.5*iqr)) | dat[,x] > (q3 + (1.5*iqr)), 1,0)
  tab = rbind(
    summary(dat[,x]),
    summary(dat[mark==0, x])
  )
  return(tab)
}
# remove admin vars
numAdminVars <- c("metadata.deviceID", "oafid", "X")
numVarsNotAdmin <- numVars[!numVars %in% numAdminVars]
iqrTab <- do.call(plyr::rbind.fill, lapply(numVarsNotAdmin, function(y){
  #print(y)
  res = iqr.check(d, y)
  #print(dim(res))
  out = data.frame(var=rbind(y, paste(y, ".iqr", sep="")), res)
  return(out)
}))
iqrTab[,2:8] <- sapply(iqrTab[,2:8], function(x){round(x,1)})

The outlier table summarizes the numeric variables with and without IQR outliers to show how the data changes based on this filter.

TODO - check the composition of the fertilizer/acre variables.

knitr::kable(iqrTab, row.names = F, digits = 0, format = 'markdown')

var	Min.	X1st.Qu.	Median	Mean	X3rd.Qu.	Max.	NA.s
oaf	0	0	0	0	1	1	2
oaf.iqr	0	0	0	0	1	1	2
age	5	35	45	101	56	63820	6
age.iqr	5	35	45	46	56	87	6
respondent.gender	0	0	1	1	1	1	2
respondent.gender.iqr	0	0	1	1	1	1	2
hhsize	0	4	6	6	7	66	2
hhsize.iqr	0	4	6	6	7	11	2
seasons.oaf	0	0	1	2	3	9	2
seasons.oaf.iqr	0	0	1	2	3	7	2
cows	0	0	2	2	3	20	1
cows.iqr	0	0	2	2	3	7	1
goats	0	0	0	1	0	14	1
goats.iqr	0	0	0	0	0	0	1
chickens	0	3	6	9	11	300	1
chickens.iqr	0	3	6	7	10	23	1
pigs	0	0	0	0	0	30	8
pigs.iqr	0	0	0	0	0	0	8
sheep	0	0	0	0	0	25	1
sheep.iqr	0	0	0	0	0	0	1
plot.size	0	0	0	0	0	2	2
plot.size.iqr	0	0	0	0	0	1	2
seed.kgs	0	3	4	5	6	100	56
seed.kgs.iqr	0	3	4	4	6	10	56
yield	0	2	5	17	9	1120	56
yield.iqr	0	2	4	5	7	19	56
harvestcomp.2016	1	1	2	2	2	3	48
harvestcomp.2016.iqr	1	1	2	2	2	3	48
intercrop.seed.kgs	0	2	4	5	6	60	810
intercrop.seed.kgs.iqr	0	2	4	5	6	12	810
intercrop.yield	0	3	8	12	20	104	812
intercrop.yield.iqr	0	2	8	11	20	45	812
intercrop.harvestcomp	1	1	2	2	2	3	805
intercrop.harvestcomp.iqr	1	1	2	2	2	3	805
dap.main	0	10	25	23	25	200	240
dap.main.iqr	0	10	16	18	25	46	240
can.main	0	12	25	24	25	200	677
can.main.iqr	0	10	25	18	25	42	677
npk.main	3	20	50	37	50	100	1924
npk.main.iqr	3	16	38	32	50	50	1924
urea.main	1	4	6	12	10	100	1878
urea.main.iqr	1	4	5	5	8	12	1878
dap.intercrop	0	5	10	13	12	125	1658
dap.intercrop.iqr	0	4	8	7	10	20	1658
can.intercrop	0	5	8	12	12	125	1856
can.intercrop.iqr	0	4	6	7	10	20	1856
npk.intercrop	25	31	38	38	44	50	1935
npk.intercrop.iqr	25	31	38	38	44	50	1935
urea.intercrop	0	2	3	3	4	5	1933
urea.intercrop.iqr	0	2	3	3	4	5	1933
compost.kgs	0	0	0	77	80	12000	54
compost.kgs.iqr	0	0	0	33	50	200	54
lime.kgs	4	10	12	29	25	150	1901
lime.kgs.iqr	4	9	12	15	23	38	1901
slope	0	5	5	7	10	45	2
slope.iqr	0	5	5	6	10	17	2
plot.m2	253	1012	2023	2113	2023	8092	2
plot.m2.iqr	253	1012	2023	1578	2023	3034	2
can.acre	-132	32	50	47	50	200	677
can.acre.iqr	5	25	50	41	50	77	677
dap.acre	-132	32	50	47	50	400	240
dap.acre.iqr	5	25	50	40	50	77	240
npk.acre	6	33	50	62	100	200	1924
npk.acre.iqr	6	33	50	62	100	200	1924
urea.acre	1	8	16	21	24	100	1878
urea.acre.iqr	1	8	16	15	20	40	1878
compost.acre	-1584	0	0	187	180	48000	37
compost.acre.iqr	-198	0	0	61	80	450	37
seed.acre	-79	8	10	12	12	640	55
seed.acre.iqr	3	8	9	10	12	18	55
intercrop.seed.acre	-79	7	9	12	16	120	809
intercrop.seed.acre.iqr	0	6	8	10	14	30	809
intercrop.dap.acre	-198	10	20	25	40	100	1657
intercrop.dap.acre.iqr	0	10	20	24	40	80	1657
intercrop.can.acre	-132	8	20	24	40	100	1855
intercrop.can.acre.iqr	0	9	20	24	37	64	1855
intercrop.npk.acre	25	31	38	38	44	50	1935
intercrop.npk.acre.iqr	25	31	38	38	44	50	1935
intercrop.urea.acre	0	6	9	8	12	16	1933
intercrop.urea.acre.iqr	0	6	9	8	12	16	1933
yield.kg	4	135	300	489	540	40000	80
yield.kg.iqr	4	135	270	340	495	1120	80
pH	0	5	6	6	6	8	34
pH.iqr	4	5	6	6	6	6	34
X.EC..Salts.	31	64	74	Inf	84	Inf	34
X.EC..Salts..iqr	34	64	74	74	84	115	34
Phosphorus	2	7	10	Inf	15	Inf	34
Phosphorus.iqr	2	7	10	11	14	28	34
Potassium	0	104	142	162	204	1104	34
Potassium.iqr	0	103	140	155	197	353	34
Calcium	0	581	901	1039	1292	8131	34
Calcium.iqr	0	568	872	936	1223	2337	34
Magnesium	0	102	151	172	216	964	34
Magnesium.iqr	0	100	148	162	209	387	34
Sulphur	4	9	11	Inf	12	Inf	34
Sulphur.iqr	5	9	11	11	12	16	34
Copper	0	2	3	4	5	16	34
Copper.iqr	0	2	3	4	5	9	34
Boron	0	0	0	0	0	1	34
Boron.iqr	0	0	0	0	0	1	34
Zinc	0	5	6	6	8	18	34
Zinc.iqr	2	5	6	6	8	11	34
X.Sodium	0	4	7	Inf	12	Inf	34
X.Sodium.iqr	0	4	6	8	11	24	34
Iron	94	132	144	Inf	158	Inf	34
Iron.iqr	94	132	144	145	156	196	34
X.C.E.C	0	7	10	11	14	49	34
X.C.E.C.iqr	0	7	10	11	14	23	34
X.Exchangeable.Aluminium	0	0	0	Inf	0	Inf	34
X.Exchangeable.Aluminium.iqr	0	0	0	0	0	0	34
X.Exchangeable.Acidity	0	0	0	Inf	0	Inf	34
X.Exchangeable.Acidity.iqr	0	0	0	0	0	0	34
X.Phosphorus.Sorption.Index..PSI.	0	83	118	127	161	411	34
X.Phosphorus.Sorption.Index..PSI..iqr	0	82	116	123	158	274	34
X.Organic.Carbon	0	2	2	2	2	3	34
X.Organic.Carbon.iqr	1	2	2	2	2	3	34
Manganese	66	172	267	260	338	498	34
Manganese.iqr	66	172	267	260	338	498	34
Aluminium	522	941	1073	1046	1164	1508	34
Aluminium.iqr	609	946	1076	1052	1165	1495	34
X.Total.Nitrogen	0	0	0	0	0	0	34
X.Total.Nitrogen.iqr	0	0	0	0	0	0	34

3.7.2 Outlier Graphs

# http://rforpublichealth.blogspot.com/2014/02/ggplot2-cheatsheet-for-visualizing.html
for(i in 1:length(numVarsNotAdmin)){
    base <- ggplot(d, aes(x=d[,numVarsNotAdmin[i]])) + labs(x = numVarsNotAdmin[i])
    temp1 <- base + geom_density()
    temp2 <- base + geom_histogram()
    #temp2 <- boxplot(r[,numVars[i]],main=paste0("Variable: ", numVars[i]))
    multiplot(temp1, temp2, cols = 2)
}

3.7.3 Clean soil values

Before aligning them with the baseline soil values

check.3sd <- function(x) {
  x = ifelse(is.infinite(x), NA, x)
  mean = mean(x, na.rm=T)
  sd = sd(x, na.rm=T)
  mark = ifelse(x>(mean + (3*sd)) |
        x<(mean - (3*sd)), NA, x)
  return(mark)
}
sdSoilVals <- d %>%
  dplyr::select(pH:X.Total.Nitrogen) 
sdCheck <- as.data.frame(apply(sdSoilVals, 2, function(x){
  return(check.3sd(x))
}))

for(i in 1:length(soilVars)){
  print(ggplot(data=sdCheck, aes(x=sdCheck[,soilVars[i]])) + 
    geom_density() + 
    labs(x=soilVars[i])
  )
}

Important note: I’m going to add the adjusted values to the r data frame giving the previous variables the extension .raw so I can distinguish between the original and modified data.

names(d)[which(names(d)=="pH"):which(names(d)=="X.Total.Nitrogen")] <- paste0(names(d)[which(names(d)=="pH"):which(names(d)=="X.Total.Nitrogen")], ".raw")
d <- cbind(d, sdCheck)

3.8 Check round 1 ids

Check for unique ids in the round 1 data

length(d$Soil_Sample_Id)==length(unique(d$Soil_Sample_Id))

[1] FALSE

dups <- d$Soil_Sample_Id[duplicated(d$Soil_Sample_Id) & !is.na(d$Soil_Sample_Id)]

Let’s use the baseline data to resolve these duplicated ids

roundId <- d %>%
  dplyr::select(district, site, Soil_Sample_Id) %>%
  filter(d$Soil_Sample_Id %in% dups) %>%
  filter(!is.na(district) & !is.na(Soil_Sample_Id))

The first one is marked as both OAF and not OAF in the follow up. The surveys happened on consecutive days. I’m going to keep the obersvation with the same phone number from the baseline.

# duplicated id 1
idCheck <- d[d$Soil_Sample_Id %in% dups[1],]
bCheck <- b[b$Soil_Sample_Id %in% dups[1],]
d <- d[-which(d$Soil_Sample_Id==dups[1] & d$phone!=724903366),]

I think the second survey more closely resembles the baseline version of this farmer in the data. I’m keeping the survey done by Lazarus.

#duplicated id 2
idCheck <- d[d$Soil_Sample_Id %in% dups[2],]
bCheck <- b[b$Soil_Sample_Id %in% dups[2],]
d <- d[-which(d$Soil_Sample_Id==dups[2] & d$metadata.username!="lazarus.m"),]

The age and the GPS coordinate indicate that the survey with the age of 54 is probably the right one.

#duplicated id 3
idCheck <- d[d$Soil_Sample_Id %in% dups[3],]
bCheck <- b[b$Soil_Sample_Id %in% dups[3],]
d <- d[-which(d$Soil_Sample_Id==dups[3] & d$age!=54),]

Quick check of the work. There are still Soil_Sample_Id that are missing. Most of them have a new soil sample id but not all.

TODO - check with Charles as to why someone might not have a Soil_Sample_Id from the baseline but would have a new Soil_Sample_Id in round 1.

There are not that many new soil sample ids so perhaps it was a way to add more farmers to the sample?

length(d$Soil_Sample_Id)==length(unique(d$Soil_Sample_Id))

[1] FALSE

table(is.na(d$Soil_Sample_Id))

FALSE  TRUE 
 1872    62 

#d[is.na(d$Soil_Sample_Id),]

FOR THE TIME BEING: drop those missing a soil sample id in round 1.

d <- d[-which(is.na(d$Soil_Sample_Id)),]

3.9 Align baseline and round 1 vars

I’ll do a couple things:

• Add season variable for eventual rbind
• Variable names to lowercase
• Change baseline variable names to match follow up.
• resolve duplicates in the baseline data (where’d the come from?)

3.9.1 Baseline duplicates

length(b$Soil_Sample_Id)==length(unique(b$Soil_Sample_Id))

[1] FALSE

dups <- b$Soil_Sample_Id[duplicated(b$Soil_Sample_Id) & !is.na(b$Soil_Sample_Id)]

Resolve them here. They all appear to be control values that were used twice. Can I assign them a new control value? Probably not. See who they followed up with the first round to know which one to keep.

#b[b$soil_sample_id=="c330",] # not clear
#b[b$soil_sample_id=="c384",] # it's exactly the same, drop one
#b[b$soil_sample_id=="c1129",] # it's exactly the same, drop one
#b[b$soil_sample_id=="c626",] # not clear
#b[b$soil_sample_id=="c856",] # it's exactly the same, drop one
dropOne <- c("c384", "c1129", "c856")
b$n <- ave(1:length(b$Soil_Sample_Id), b$Soil_Sample_Id, FUN = seq_along)
b$drop <- ifelse(b$n==2 & b$Soil_Sample_Id %in% dropOne, 1, 0)
b <- b[-which(b$drop==1),]
  
dropForNow <- c("c330", "c626") # see below

TODO - confirm the data cleaning process at the baseline so that the soil data variables are being treated the same way in the baseline and round 1. They should probably be cleaned separately but should be treated the same way.

d$season <- "2016"
b$season <- "2015"
names(d) <- tolower(names(d))
names(b) <- tolower(names(b))
bUpdate <- b %>% rename(
  region = regionname,
  district = districtname,
  site = sitename,
  respondent.gender = gender, # check that this is correct
  plot.location = field_location,
  plot.size = field_size,
  harvestcomp.2016 = yield_comparative,
  main.crop = plot_information.maincrop,
  main.crop.specify = plot_information.specify_other_main_crop,
  seed.type = seedtype, 
  seed.kgs = seedkgs,
  intercrop = intercrop.intercrop,
  intercrop.specify = intercrop.specify_other_main_crop,
  intercrop.seed.type = intercrop.seedtype,
  intercrop.seed.kgs = intercrop.seedkgs,
  intercrop.harvestcomp = intercrop.yield_comparative,
  fertilizer.main = inputs.input_maincrop,
  dap.main = inputs.dap_kg,
  can.main = inputs.can_kg,
  npk.main = inputs.npk_kg,
  urea.main = inputs.urea_kg,
  fertilizer.intercrop = inputs.input_intercrop,
  dap.intercrop = inputs.dap_kg_intercrop,
  can.intercrop = inputs.can_kg_intercrop,
  npk.intercrop = inputs.npk_kg_intercrop,
  urea.intercrop = inputs.urea_kg_intercrop,
  compost.kgs = inputs.compost,
  compost.quality = inputs.compost_quality,
  compost.type = inputs.compost_type,
  lime = inputs.lime,
  lime.kgs = inputs.lime_kg,
  soil.type = soil_type,
  soil.color = soil_color,
  erosion = anti_erosion,
  field.location = location,
  seasons.oaf = seasons_oaf,
  x.c.e.c = c.e.c,
  copper = cu,
  x.ec..salts. = ec,
  #x.exchangeable.aluminum = exch.al,
  x.phosphorus.sorption.index..psi. = psi,
  potassium = k,
  magnesium = mg,
  manganese = mn,
  boron = b,
  calcium = ca,
  iron = fe,
  x.sodium = na,
  phosphorus = p, 
  sulphur = s,
  zinc = zn,
  x.organic.carbon = total.c,
  x.total.nitrogen = total.n,
  x.exchangeable.aluminium = exch.al
)
# helper to know what else needs to be changed
names(d)[!names(d) %in% names(bUpdate)]

 [1] "appformid"                             "id"                                    "domain"                               
 [4] "date_header"                           "metadata.deviceid"                     "metadata.userid"                      
 [7] "metadata.username"                     "metadata.timestart"                    "metadata.timeend"                     
[10] "form.case.@case_id"                    "same.hh"                               "agree"                                
[13] "interviewed.2016"                      "refusal"                               "phone"                                
[16] "district1"                             "site1"                                 "participation"                        
[19] "hhsize"                                "which.seasons"                         "own"                                  
[22] "relation.land"                         "own.2016"                              "most.farming"                         
[25] "yield.unit"                            "intercrop.yield.unit"                  "fertility.comp"                       
[28] "fallow.yn"                             "fallow.cover"                          "residues"                             
[31] "slope"                                 "sampling.barcode"                      "comment"                              
[34] "#form/sampling2017_complete"           "new_soil_sample_id"                    "plot.m2"                              
[37] "seed.acre"                             "intercrop.seed.acre"                   "intercrop.dap.acre"                   
[40] "intercrop.can.acre"                    "intercrop.npk.acre"                    "intercrop.urea.acre"                  
[43] "yield.kg"                              "ph.raw"                                "x.ec..salts..raw"                     
[46] "phosphorus.raw"                        "potassium.raw"                         "calcium.raw"                          
[49] "magnesium.raw"                         "sulphur.raw"                           "copper.raw"                           
[52] "boron.raw"                             "zinc.raw"                              "x.sodium.raw"                         
[55] "iron.raw"                              "x.c.e.c.raw"                           "x.exchangeable.aluminium.raw"         
[58] "x.exchangeable.acidity.raw"            "x.phosphorus.sorption.index..psi..raw" "x.organic.carbon.raw"                 
[61] "manganese.raw"                         "aluminium.raw"                         "x.total.nitrogen.raw"                 
[64] "x.exchangeable.acidity"                "aluminium"                            

names(bUpdate)[!names(bUpdate) %in% names(d)]

 [1] "ssn"                        "info.formid"                "last_name"                  "first_name"                
 [5] "clientphone"                "seasons_oaf_specify"        "chemical_fertilizer_5"      "why_no_chemical_fertilizer"
 [9] "compost_fertilizer_5"       "why_no_compost"             "lime_fertilizer_5"          "why_no_lime"               
[13] "fertilizer_5"               "legum_maincrop_5"           "legum_intercrop_5"          "crop_rese"                 
[17] "fertile_comparison"         "globalclientid"             "soil_sampling_complete"     "info.caseid"               
[21] "info.completed_time"        "info.username"              "info.started_time"          "date.sampled"              
[25] "oaf_id"                     "hp"                         "lat"                        "lon"                       
[29] "alt"                        "precision"                  "valley"                     "hilltop"                   
[33] "hillside"                   "crop.maize"                 "dap.check"                  "field_size.adj"            
[37] "seasons_breaks"             "own.cows"                   "own.goats"                  "own.chickens"              
[41] "own.pigs"                   "own.sheep"                  "clay_soil"                  "loam_soil"                 
[45] "sandy_soil"                 "n"                          "drop"                      

The variables that remain to be aligned are the soil variables and any resulting calulations such as fertilizer per acre. These caculations can be redone once the data is combined.

Make groups of variables to make them easier to find later

historicalBaseline <- names(b)[which(names(b)=="chemical_fertilizer_5"):which(names(b)=="legum_intercrop_5")]
baselineSoilVars <- names(b)[which(names(b)=="c.e.c"):which(names(b)=="total.n")]

3.10 Combine baseline and round 1

d <- d %>%
  mutate(
    soil_sample_id = tolower(gsub(" ", "", soil_sample_id))
  )
commonVars <- names(d)[names(d) %in% names(bUpdate)] 
write.csv(commonVars, file="varNamesforM&E.csv")
m2ToAcres <- function(input, meters) {
  res <- (input/meters)*4046
  return(res)
}
# check soil sample id matches before rbind
table(d$soil_sample_id %in% bUpdate$soil_sample_id)

FALSE  TRUE 
   32  1840 

d$soil_sample_id[!d$soil_sample_id %in% bUpdate$soil_sample_id]

 [1] "lugari52284"           "busia33787"            "c1136"                 "gem45918"              "c703"                 
 [6] "busia34175"            "butere49984"           "migori14465"           "kakamegab(north)61463" "rongo33010"           
[11] "webuye53326"           "rachuonyo22477"        "c863"                  "rachuonyo16330"        "rongo35982"           
[16] "c241"                  "c290"                  "migori17557"           "gem64358"              "matete54668"          
[21] "kisii43004"            "kakamegab(north)15878" "webuye52641"           "gem57424"              "suneka16515"          
[26] "kakamegab(north)63510" "c857"                  "rachuonyo42533"        "rachuonyo39005"        "suneka30533"          
[31] "rachuonyo40077"        "kakamegab(north)6413" 

table(bUpdate$soil_sample_id %in% d$soil_sample_id)

FALSE  TRUE 
  190  1842 

bUpdate$soil_sample_id[!bUpdate$soil_sample_id %in% d$soil_sample_id]

  [1] "busia27558"            "busia25200"            "c27"                   "c198"                  "c207"                 
  [6] "c208"                  "c209"                  "c215"                  "c240"                  "matete15959"          
 [11] "matete57201"           "c795"                  "c797"                  "c802"                  "c807"                 
 [16] "c835"                  "c841"                  "kakamegab(north)45636" "kakamegab(north)54395" "kakamegab(north)55666"
 [21] "kakamegab(north)57759" "c526"                  "c555"                  "c556"                  "c557"                 
 [26] "c558"                  "c559"                  "c560"                  "c561"                  "c562"                 
 [31] "c563"                  "c565"                  "c566"                  "c567"                  "c568"                 
 [36] "c569"                  "c570"                  "c571"                  "c572"                  "c573"                 
 [41] "c574"                  "c575"                  "c576"                  "c577"                  "c578"                 
 [46] "c579"                  "c581"                  "c582"                  "c583"                  "c584"                 
 [51] "c585"                  "c586"                  "c587"                  "c591"                  "c597"                 
 [56] "c604"                  "lugari65731"           "lugari66391"           "c695"                  "c704"                 
 [61] "c707"                  "c721"                  "c731"                  "c736"                  "c744"                 
 [66] "c770"                  "c775"                  "c780"                  "c784"                  "butere15379"          
 [71] "butere50525"           "butere56919"           "butere57046"           "butere55190"           "butere51928"          
 [76] "butere56266"           "c127"                  "c77"                   "c121"                  "c162"                 
 [81] "c63"                   "c152"                  "c153"                  "c154"                  "c61"                  
 [86] "c124"                  "c114"                  "c93"                   "c135"                  "c69"                  
 [91] "c57"                   "c84"                   "c155"                  "c71"                   "c163"                 
 [96] "gem60104"              "gem51405"              "gem57253"              "c301"                  "c270"                 
[101] "c357"                  "c249"                  "c396"                  "c266"                  "c373"                 
[106] "c282"                  "c331"                  "c281"                  "c397"                  "c398"                 
[111] "c272"                  "c393"                  "c259"                  "c375"                  "webuye33853"          
[116] "c1220"                 "kakamega(south)52107"  "kakamega(south)55651"  "kakamega(south)61334"  "c490"                 
[121] "c499"                  "c475"                  "c459"                  "c470"                  "c410"                 
[126] "c488"                  "rachuonyo30231"        "rachuonyo41225"        "c1014"                 "c982"                 
[131] "c1054"                 "c980"                  "c1021"                 "c1055"                 "suneka32800"          
[136] "suneka33096"           "suneka30964"           "suneka29770"           "suneka31042"           "c1159"                
[141] "c1161"                 "c1187"                 "rongo27024"            "rongo29226"            "rongo19791"           
[146] "rongo18810"            "rongo33013"            "c1133"                 "c1117"                 "c1137"                
[151] "c1140"                 "c1106"                 "c1138"                 "c1134"                 "c1125"                
[156] "c1118"                 "c1126"                 "c1149"                 "c1147"                 "c1095"                
[161] "c1135"                 "c1139"                 "c1143"                 "kisii41906"            "kisii41862"           
[166] "c643"                  "c682"                  "c665"                  "migori5694"            "migori18384"          
[171] "migori9269"            "migori18010"           "migori10391"           "c882"                  "c898"                 
[176] "c899"                  "c910"                  "c928"                  "c884"                  "c960"                 
[181] "c935"                  "c922"                  "c914"                  "c936"                  "c867"                 
[186] "c880"                  "c870"                  "c883"                  "c858"                  "c1240"                

fieldDat <- rbind(bUpdate[,commonVars], d[,commonVars])
fieldDat <- fieldDat %>% mutate(
  plot.m2 = plot.size*4046,
  can.acre = m2ToAcres(can.main, plot.m2),
  dap.acre = m2ToAcres(dap.main,plot.m2),
  npk.acre = m2ToAcres(npk.main,plot.m2),
  urea.acre = m2ToAcres(urea.main,plot.m2),
  compost.acre = m2ToAcres(compost.kgs,plot.m2),
  seed.acre = m2ToAcres(seed.kgs,plot.m2),
  intercrop.seed.acre = m2ToAcres(intercrop.seed.kgs, plot.m2),
  intercrop.dap.acre = m2ToAcres(dap.intercrop, plot.m2),
  intercrop.can.acre = m2ToAcres(can.intercrop, plot.m2),
  intercrop.npk.acre = m2ToAcres(npk.intercrop, plot.m2),
  intercrop.urea.acre = m2ToAcres(urea.intercrop, plot.m2)
) %>% rename(
  d_client = oaf,
  sample_id = soil_sample_id
)
# drop the ids that are duplicates
fieldDat <- fieldDat[!fieldDat$sample_id %in% dropForNow,]

Check that categorical variable responses align between the baseline and round 1.

catVars <- names(fieldDat)[sapply(fieldDat, function(x){
  is.character(x)
})]
fieldNonAdmin <- catVars[!catVars %in% c("plot.location", "gps", "sample_id", "main.crop.specify", "intercrop.specify", "photo", "site")]
fieldDat$region <- ifelse(grepl("nyan", tolower(fieldDat$region)), "Nyanza", "Western")
for(i in 1:length(fieldNonAdmin)){
  repGraphs(fieldDat, fieldNonAdmin[i])
}

TODO

• reality check the data cleaning and management process between baseline and round 1, make sure they’re the same.
• reality check the append
• reality check GPS

4 Analysis

The aim of the analysis is to:

TODO

• Check movement in the sample
• resolve duplicates in the baseline (see below!)
• cut straight to the tables in the report ala Rwanda

4.1 Client movement

fieldDat %>%
  dplyr::select(sample_id, season, d_client) %>%
  group_by(sample_id) %>%
  spread(., season, d_client) %>%
  rename(
    client15 = `2015`,
    client16 = `2016`
  ) %>%
  mutate(
    becameClient = ifelse(client15==0 & client16==1, 1, 0),
    becameControl = ifelse(client15==1 & client16==0, 1, 0),
    stayedClient = ifelse(client15==1 & client16==1, 1, 0),
    stayedControl = ifelse(client15==0 & client16==0, 1, 0)
  ) %>% 
  ungroup() %>%
  dplyr::summarize_each(
    funs(mean= mean(., na.rm=T)), -c(sample_id, client15, client16)
  ) %>% 
  mutate_each(
    funs(paste0(round(.,2)*100, "%"))
  ) %>%
  kable(caption="Movement in Sample", format='markdown')

becameClient_mean	becameControl_mean	stayedClient_mean	stayedControl_mean
4%	11%	38%	42%

4.2 Client counts

4.2.1 Regressions

See sketch of SHS report.

TODO - START HERE

• run regression
• bring in yield values, merge soil vales, follow the other template
• produce remaining tables

Consider including:

• time FEs
• age and a squared age term
• gender (absorbed by fixed effects)
• years of education (absorbed by fixed effects)
• bootstrapped st. errors / robust standard errors

Helpful link for executing code in parallel

if(!file.exists(regFile) || forceUpdate) {
library(parallel)
no_cores <- detectCores() - 1
cl <- makeCluster(no_cores, type="FORK")
clusterEvalQ(cl, "plm")
clusterExport(cl, "fieldSoilDat")
clusterExport(cl, "keySoilVars")
clusterExport(cl, "indFeList")
indFeLoop <- parLapply(cl, indFeList, function(mod){
  lapply(keySoilVars, function(outcome){
    form = lm(reformulate(termlabels = mod, response = outcome), data=fieldSoilDat)
    
    pdf(file=paste("output/", paste0(outcome, paste(mod, collapse = "")), ".pdf", sep = "")) 
    print(plot(form))
    dev.off()
    
    form = plm(form, c("sample_id", "age", "age2"))
    
    rownames(form) = paste(rownames(form), outcome, sep = " ")
    return(form)
  })
  
})
stopCluster(cl)
save(indFeLoop, file=regFile)
} else {
  load("regFile.RData")
}

not plotting observations with leverage one:
  138, 146, 159, 165, 215, 222, 227, 256, 292, 299, 308, 337, 364, 365, 366, 367, 368, 371, 376, 377, 379, 381, 384, 386, 387, 388, 391, 395, 398, 504, 520, 528, 530, 539, 554, 561, 580, 586, 596, 659, 674, 728, 752, 754, 781, 792, 811, 815, 820, 824, 873, 974, 994, 1013, 1015, 1022, 1027, 1029, 1043, 1050, 1077, 1089, 1092, 1107, 1121, 1144, 1152, 1207, 1262, 1279, 1350, 1353, 1355, 1398, 1405, 1445, 1452, 1483, 1526, 1538, 1541, 1560, 1565, 1610, 1633, 1638, 1669, 1671, 1684, 1699, 1722, 1724, 1725, 1734, 1735, 1736, 1743, 1755, 1758, 1791, 1795, 1797, 1808, 1844, 1847, 1862, 1878, 1883, 1895, 1935, 1937, 1949, 1954, 1966, 1969, 1978, 1989, 1991, 1996, 2019, 2544, 2600, 2609, 2767, 2792, 2830, 3038, 3583, 3618, 3682, 3716, 3768, 3807

And combine model outputs into tables for each model

In the individual fixed effect model above, the naive model would only include a client indicator and individual fixed effects. If we add season, we lose significance on almost everything. I’d guess that as we add more likely controls we additionally lose signficance. I’ve included age and age squared along the lines of Hicks et.al.

	Coefficient	95% Confidence Interval	P-Value
(Intercept) ph	5.5000	5 to 6	<0.001 ***
as.factor(d_client)1 ph	-0.0330	-0.087 to 0.021	0.24
as.factor(season)2016 ph	-0.3900	-0.41 to -0.36	<0.001 ***
(Intercept) calcium	440.0000	-160 to 1000	0.15
as.factor(d_client)1 calcium	-34.0000	-100 to 36	0.34
as.factor(season)2016 calcium	-56.0000	-84 to -28	<0.001 ***
(Intercept) magnesium	74.0000	-0.84 to 150	0.053 .
as.factor(d_client)1 magnesium	-5.7000	-14 to 3	0.2
as.factor(season)2016 magnesium	-14.0000	-17 to -10	<0.001 ***
(Intercept) x.organic.carbon	1.2000	0.77 to 1.6	<0.001 ***
as.factor(d_client)1 x.organic.carbon	0.0170	-0.033 to 0.067	0.5
as.factor(season)2016 x.organic.carbon	-0.3100	-0.33 to -0.29	<0.001 ***
(Intercept) x.total.nitrogen	0.1000	0.074 to 0.13	<0.001 ***
as.factor(d_client)1 x.total.nitrogen	-0.0032	-0.0063 to -1.5e-05	0.049 *
as.factor(season)2016 x.total.nitrogen	-0.0110	-0.012 to -0.0099	<0.001 ***

5 Summary

6 Appendix